Aiming at the near infrared spectra (NIR) on local effect sensitivity, numerous predictor variables with serious multicollinearity and having nonlinear quantitative relationship with the chemical compositions from the spectral data, a novel ensemble model, termed as ensemble model based on the subbaggin technique and quadratic partial least squares regression ( E-S-QPLSR), was constructed. Firstly, a quite quantity of forecasting sub-models had been established by using the non-linear quadratic partial least squares regression (QPLSR) method and the subagging algorithm, that was a subsampling technique without replacement from the training samples. Then, based on the groups of the training samples forecasting values from the above sub-models, all of the sub-model weighting cocefficients were calculated by using the linear PLSR algorithm. Finally, the application to the corn samples water content modeling of the proposed E-S-QPLSR method was presented in comparison with some other methods. The E-S-QPLSR method not only holds on fine learning ability, but also improves the prediction performance and steady capability.